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Research: Tracing human stem cell lineage during development using DNA methylation
- Lucas A. Salas,
- John K. Wiencke,
- Devin C. Koestler,
- Ze Zhang,
- Brock C. Christensen,
- and Karl T. Kelsey
Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
...with FCO levels ≥3%, this correlation between FCO and age was no longer significant (r = −0.12, P > 0.05). Of further note, there was no overlap in the loci comprising the FCO signature with the previously described CpGs used to calculate DNA methylation age (Lowe et al. 2016). Although age associated...
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Resource: A DNA methylation fingerprint of 1628 human samples
- Agustin F. Fernandez,
- Yassen Assenov,
- Jose Ignacio Martin-Subero,
- Balazs Balint,
- Reiner Siebert,
- Hiroaki Taniguchi,
- Hiroyuki Yamamoto,
- Manuel Hidalgo,
- Aik-Choon Tan,
- Oliver Galm,
- Isidre Ferrer,
- Montse Sanchez-Cespedes,
- Alberto Villanueva,
- Javier Carmona,
- Jose V. Sanchez-Mut,
- Maria Berdasco,
- Victor Moreno,
- Gabriel Capella,
- David Monk,
- Esteban Ballestar,
- Santiago Ropero,
- Ramon Martinez,
- Marta Sanchez-Carbayo,
- Felipe Prosper,
- Xabier Agirre,
- Mario F. Fraga,
- Osvaldo Graña,
- Luis Perez-Jurado,
- Jaume Mora,
- Susana Puig,
- Jaime Prat,
- Lina Badimon,
- Annibale A. Puca,
- Stephen J. Meltzer,
- Thomas Lengauer,
- John Bridgewater,
- Christoph Bock,
- and Manel Esteller
Genome Res. February 2012 22: 407-419; Published in Advance May 25, 2011, doi:10.1101/gr.119867.110
..., Spain AbstractMost of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
...about their contribution to natural human variation. To determine their contribution to variability, we have generated genome-scale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both...
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Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
...,417 divergent. Of the homoscedastic CpG sites, 92,074 showed LV in both young and old individuals and 92,753 showed HV in both populations (Fig. 4B,C).View larger version: In this window In a new window Figure 4. Interindividual DNA methylation variability during aging of blood cells. (A) Density plot for Cp...
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Research: The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes
- Ai Ling Teh,
- Hong Pan,
- Li Chen,
- Mei-Lyn Ong,
- Shaillay Dogra,
- Johnny Wong,
- Julia L. MacIsaac,
- Sarah M. Mah,
- Lisa M. McEwen,
- Seang-Mei Saw,
- Keith M. Godfrey,
- Yap-Seng Chong,
- Kenneth Kwek,
- Chee-Keong Kwoh,
- Shu-E. Soh,
- Mary F.F. Chong,
- Sheila Barton,
- Neerja Karnani,
- Clara Y. Cheong,
- Jan Paul Buschdorf,
- Walter Stünkel,
- Michael S. Kobor,
- Michael J. Meaney,
- Peter D. Gluckman,
- and Joanna D. Holbrook
Genome Res. July 2014 24: 1064-1074; Published in Advance April 7, 2014, doi:10.1101/gr.171439.113
...pregnancy and offspring adiposity at 9 yr of age associate with the DNA methylation level of the RXRA promoter in the umbilical cord (Godfrey et al. 2011). There are examples of persistent, environmentally induced DNA methylation states. For instance, variations in maternal care alter the methylation...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
..., answering this question is important for understanding the potential of DNA methylation–based episignatures (Aref-Eshghi et al. 2021; Levy et al. 2022a) to shed light on the pathogenesis of the disorders. Although these episignatures are almost exclusively derived from whole blood, there is increasing...

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